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Patch rev complement and first implementation of --auto in obicsv

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Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
This commit is contained in:
Eric Coissac
2023-11-07 09:37:07 +02:00
parent 6a6a6f6f2c
commit 61c30f9b6a
21 changed files with 270 additions and 107 deletions
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19
pkg/obiseq/revcomp.go
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@@ -1,7 +1,17 @@
package obiseq
// ".ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]"
var _revcmpDNA = []byte(".TVGHEFCDIJMLKNOPQYSAABWXRZ#!][")
var _revcmpDNA = []byte(".TVGHNNCDNNMNKNNNNYSAABWNRN]N[NNN")
func complement(n byte) byte {
switch {
case n == '.' || n == '-':
return n
case (n >= 'A' && n <= 'z'):
return _revcmpDNA[n&31] | (n & 0x20)
}
return 'n'
}
// Reverse complements a DNA sequence.
// If the inplace parametter is true, that operation is done in place.
@@ -18,8 +28,7 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
// ASCII code & 31 -> builds an index in witch (a|A) is 1
// ASCII code & 0x20 -> Foce lower case
s[j], s[i] = _revcmpDNA[s[i]&31]|(s[i]&0x20),
_revcmpDNA[s[j]&31]|(s[j]&0x20)
s[j], s[i] = complement(s[i]), complement(s[j])
j++
}
@@ -40,8 +49,7 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
b := []byte(m)
// Echange and reverse complement symboles
b[1], b[9] = _revcmpDNA[b[9]&31]|(b[9]&0x20),
_revcmpDNA[b[1]&31]|(b[1]&0x20)
b[1], b[9] = complement(b[9]), complement(b[1])
// Exchange sequencing scores
b[3], b[4], b[11], b[12] = b[11], b[12], b[3], b[4]
@@ -65,7 +73,6 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
return sequence
}
func ReverseComplementWorker(inplace bool) SeqWorker {
f := func(input *BioSequence) *BioSequence {
return input.ReverseComplement(inplace)